Both seal species have gone through large population changes over the past century. The abundance of harbour seals reached an all-time low in the 1970s but subsequently increased steadily at an annual rate of 4%; however, this increase was affected by two major interruptions due to outbreaks of the phocine distemper virus (PDV) in 1988 and 2002. Over the last 15 years, declines in the harbour seal population have occurred in the northwestern North Sea. The reasons for these recent declines are unknown, although they are thought to be different in different areas. Grey seals occur predominantly along the British coasts of the North Sea and have been increasing at an annual rate of up to 10%.

Trends in the abundance of cetaceans are less well known, but it is known that the centre of summer distribution of harbour porpoises moved southwards between 1994 and 2005, possibly in response to changes in availability of main prey. Minke whales and white-beaked dolphins are found mainly in the northern North Sea, with no obvious changes in distribution between the two surveys. The resident population of bottlenose dolphins lives along the coasts of eastern Scotland and is considered to be stable or increasing.

Threatened and declining marine mammal species in the Greater North Sea according to OSPAR:​